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BioC 2.14: CHECK report for maSigPro on morelia

This page was generated on 2014-10-08 09:02:37 -0700 (Wed, 08 Oct 2014).

Package 462/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maSigPro 1.36.0
Maria Jose Nueda
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/maSigPro
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: maSigPro
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maSigPro_1.36.0.tar.gz
StartedAt: 2014-10-07 23:48:49 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:50:24 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 94.7 seconds
RetCode: 0
Status:  OK 
CheckDir: maSigPro.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maSigPro_1.36.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/maSigPro.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maSigPro/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maSigPro’ version ‘1.36.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maSigPro’ can be installed ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘stats’ ‘MASS’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
see.genes: warning in mfuzz(signif, c = k, m = m): partial argument
  match of 'c' to 'centers'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [33s/34s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
T.fit        11.312  0.729  12.014
maSigPro      7.314  0.486   7.852
get.siggenes  5.259  0.347   5.621
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/maSigPro.Rcheck/00check.log’
for details.

maSigPro.Rcheck/00install.out:

* installing *source* package ‘maSigPro’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (maSigPro)

maSigPro.Rcheck/maSigPro-Ex.timings:

nameusersystemelapsed
NBdata0.0750.0030.077
NBdesign0.0020.0010.003
PlotGroups0.0320.0030.035
PlotProfiles0.0170.0030.020
T.fit11.312 0.72912.014
average.rows0.0070.0000.008
data.abiotic0.0050.0010.006
edesign.OD0.0030.0010.003
edesign.abiotic0.0040.0010.004
edesignCT0.0020.0010.003
edesignDR0.0020.0000.003
get.siggenes5.2590.3475.621
i.rank0.0010.0000.001
maSigPro7.3140.4867.852
maSigProUsersGuide0.0070.0030.010
make.design.matrix0.0110.0060.018
p.vector3.2280.2233.458
position0.0010.0010.001
reg.coeffs0.0010.0000.002
see.genes1.2480.1531.882
stepback0.0540.0040.056
stepfor0.2090.0130.220
suma2Venn0.0090.0030.055
two.ways.stepback0.1540.0100.162
two.ways.stepfor0.2040.0120.215